Recently, sequencing costs have dropped sharply due to increased throughput, simplification, and affordability of second (or even third and fourth) generation sequencing technologies, leading to an explosion of smaller sequencing facilities. However, despite the increased rate of sequence generation, there has not been a commensurate increase in access to computational resources to support high-quality sequence processing and analysis. The Annotation Engine has been effective in providing prokaryotic annotation services to the community for four years; however the analysis needs of researchers now far exceed prokaryotic genome annotation. In this work we plan to substantially expand the analysis pipelines offered in our service to include sequence assembly, comparative genomics, and transcriptome analysis. This will result in the evolution of the Annotation Engine into the Analysis Engine. Furthermore, we will also increase the interoperability of our tools with other popular bioinformatics tools. Finally, we will engage in active outreach and training. This combination of activities is expected to enable researchers to rapidly perform analyses that are vital for public health and have significant impact in the areas of drug targeting, diagnostic marker and genotyping, infectious disease control, rapid response to pathogen outbreaks and vaccine development.